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  <div class="section" id="input-script-parameters">
<h1>Input script parameters<a class="headerlink" href="#input-script-parameters" title="Permalink to this headline">¶</a></h1>
<p>This is a list of the input parameter names recognized by
calc_dislocation_monopole.py.</p>
<div class="section" id="global-metadata-parameters">
<h2>Global metadata parameters<a class="headerlink" href="#global-metadata-parameters" title="Permalink to this headline">¶</a></h2>
<ul class="simple">
<li><p><strong>branch</strong>: assigns a group/branch descriptor to the calculation
which can help with parsing results later. Default value is ‘main’.</p></li>
</ul>
</div>
<div class="section" id="command-lines-for-lammps-and-mpi">
<h2>Command lines for LAMMPS and MPI<a class="headerlink" href="#command-lines-for-lammps-and-mpi" title="Permalink to this headline">¶</a></h2>
<p>Provides the external commands for running LAMMPS and MPI.</p>
<ul class="simple">
<li><p><strong>lammps_command</strong>: the path to the executable for running LAMMPS on
your system. Don’t include command line options.</p></li>
<li><p><strong>mpi_command</strong>: the path to the MPI executable and any command line
options to use for calling LAMMPS to run in parallel on your system.
Default value is None (run LAMMPS as a serial process).</p></li>
</ul>
</div>
<div class="section" id="potential-definition-and-directory-containing-associated-files">
<h2>Potential definition and directory containing associated files<a class="headerlink" href="#potential-definition-and-directory-containing-associated-files" title="Permalink to this headline">¶</a></h2>
<p>Provides the information associated with an interatomic potential
implemented for LAMMPS.</p>
<ul class="simple">
<li><p><strong>potential_file</strong>: the path to the potential_LAMMPS data model used
by atomman to generate the proper LAMMPS commands for an interatomic
potential.</p></li>
<li><p><strong>potential_dir</strong>: the path to the directory containing any potential
artifacts (eg. eam.alloy setfl files) that are used. If not given,
then any required files are expected to be in the working directory
where the calculation is executed.</p></li>
</ul>
</div>
<div class="section" id="initial-system-configuration-to-load">
<h2>Initial system configuration to load<a class="headerlink" href="#initial-system-configuration-to-load" title="Permalink to this headline">¶</a></h2>
<p>Provides the information associated with loading an atomic
configuration.</p>
<ul class="simple">
<li><p><strong>load_file</strong>: the path to the initial configuration file being read
in.</p></li>
<li><p><strong>load_style</strong>: the style/format for the load_file. The style can be
any file type supported by atomman.load()</p></li>
<li><p><strong>load_options</strong>: a list of key-value pairs for the optional
style-dependent arguments used by atomman.load().</p></li>
<li><p><strong>family</strong>: specifies the configuration family to associate with the
loaded file. This is typically a crystal structure/prototype
identifier that helps with linking calculations on the same material
together. If not given and the load_style is system_model, then the
family will be taken from the file if included. Otherwise, the family
will be taken as load_file stripped of path and extension.</p></li>
<li><p><strong>symbols</strong>: a space-delimited list of the potential’s atom-model
symbols to associate with the loaded system’s atom types. Required if
load_file does not contain this information.</p></li>
<li><p><strong>box_parameters</strong>: <em>Note that this parameter has no influence on
this calculation.</em> allows for the specification of new box parameters
to scale the loaded configuration by. This is useful for running
calculations based on prototype configurations that do not contain
material-specific dimensions. Can be given either as a list of three
or six numbers, with an optional unit of length at the end. If the
unit of length is not given, the specified length_unit (below) will
be used.</p>
<ul>
<li><p>a b c (unit): for orthogonal boxes.</p></li>
<li><p>a b c alpha beta gamma (unit): for triclinic boxes. The angles are
taken in degrees.</p></li>
</ul>
</li>
</ul>
</div>
<div class="section" id="elastic-constants-parameters">
<h2>Elastic constants parameters<a class="headerlink" href="#elastic-constants-parameters" title="Permalink to this headline">¶</a></h2>
<p>Specifies the computed elastic constants for the interatomic potential
and crystal structure, relative to the loaded system’s orientation.</p>
<ul class="simple">
<li><p><strong>elasticconstants_file</strong>: the path to a record containing the
elastic constants to use. If neither this or the individual Cij
components (below) are given and <em>load_style</em> is ‘system_model’, this
will be set to <em>load_file</em>.</p></li>
<li><p><strong>C11, C12, C13, C14, C15, C16, C22, C23, C24, C25, C26, C33, C34,
C35, C36, C44, C45, C46, C55, C56, C66</strong>: the individual elastic
constants components in units of pressure. If the loaded system’s
orientation is the standard setting for the crystal type, then
missing values will automatically be filled in. Example: if the
loaded system is a cubic prototype, then only C11, C12 and C44 need
be specified.</p></li>
<li><p>Isotropic moduli: the elastic constants for an isotropic material can
be defined using any two of the following</p>
<ul>
<li><p><strong>C_M</strong>: P-wave modulus (units of pressure).</p></li>
<li><p><strong>C_lambda</strong>: Lame’s first parameter (units of pressure).</p></li>
<li><p><strong>C_mu</strong>: shear modulus (units of pressure).</p></li>
<li><p><strong>C_E</strong>: Young’s modulus (units of pressure).</p></li>
<li><p><strong>C_nu</strong>: Poisson’s ratio (unitless).</p></li>
<li><p><strong>C_K</strong>: bulk modulus (units of pressure).</p></li>
</ul>
</li>
</ul>
</div>
<div class="section" id="dislocation-defect-parameters">
<h2>Dislocation defect parameters<a class="headerlink" href="#dislocation-defect-parameters" title="Permalink to this headline">¶</a></h2>
<p>Defines a unique dislocation type and orientation</p>
<ul class="simple">
<li><p><strong>dislocation_file</strong>: the path to a dislocation_monopole record file
that contains a set of input parameters associated with a specific
dislocation.</p></li>
<li><p><strong>dislocation_slip_hkl</strong>: three integers specifying the Miller (hkl)
slip plane for the dislocation.</p></li>
<li><p><strong>dislocation_Î¾_uvw</strong>: three integers specifying the Miller [uvw]
line vector direction for the dislocation. The angle between burgers
and Î¾_uvw determines the dislocation’s character</p></li>
<li><p><strong>dislocation_burgers</strong>: three floating point numbers specifying the
crystallographic Miller Burgers vector for the dislocation.</p></li>
<li><p><strong>dislocation_m</strong> three floats for the Cartesian vector of the final
system that the dislocation solution’s m vector (in-plane,
perpendicular to Î¾) should align with. Limited to being parallel to
one of the three Cartesian axes.</p></li>
<li><p><strong>dislocation_n</strong> three floats for the Cartesian vector of the final
system that the dislocation solution’s n vector (slip plane normal)
should align with. Limited to being parallel to one of the three
Cartesian axes.</p></li>
<li><p><strong>dislocation_shift</strong>: three floating point numbers specifying a
rigid body shift to apply to the atoms in the system. This controls
how the atomic positions align with the ideal position of the
dislocation core, which is at coordinates (0,0) for the two Cartesian
axes aligned with m and n.</p></li>
<li><p><strong>dislocation_shiftscale</strong>: boolean indicating if the
<em>dislocation_shift</em> value should be absolute (False) or scaled
relative to the rotated cell used to construct the system.</p></li>
<li><p><strong>dislocation_shiftindex</strong>: integer alternate to specifying shift
values, the shiftindex allows for one of the identified suggested
shift values to be used that will position the slip plane halfway
between two planes of atoms. Note that shiftindex values only shift
atoms in the slip plane normal direction and may not be the ideal
positions for some dislocation cores.</p></li>
<li><p><strong>sizemults</strong>: three integers specifying the box size multiplications
to use.</p></li>
<li><p><strong>amin</strong>: floating point number stating the minimum width along the a
direction that the system must be. The associated sizemult value will
be increased if necessary. Default value is 0.0.</p></li>
<li><p><strong>bmin</strong>: floating point number stating the minimum width along the b
direction that the system must be. The associated sizemult value will
be increased if necessary. Default value is 0.0.</p></li>
<li><p><strong>cmin</strong>: floating point number stating the minimum width along the c
direction that the system must be. The associated sizemult value will
be increased if necessary. Default value is 0.0.</p></li>
</ul>
</div>
<div class="section" id="units-for-input-output-values">
<h2>Units for input/output values<a class="headerlink" href="#units-for-input-output-values" title="Permalink to this headline">¶</a></h2>
<p>Specifies the units for various physical quantities to use when saving
values to the results record file. Also used as the default units for
parameters in this input parameter file.</p>
<ul class="simple">
<li><p><strong>length_unit</strong>: defines the unit of length for results, and input
parameters if not directly specified. Default value is ‘angstrom’.</p></li>
<li><p><strong>energy_unit</strong>: defines the unit of energy for results, and input
parameters if not directly specified. Default value is ‘eV’.</p></li>
<li><p><strong>pressure_unit</strong>: defines the unit of pressure for results, and
input parameters if not directly specified. Default value is ‘GPa’.</p></li>
<li><p><strong>force_unit</strong>: defines the unit of pressure for results, and input
parameters if not directly specified. Default value is ‘eV/angstrom’.</p></li>
</ul>
</div>
<div class="section" id="lammps-minimization-parameters">
<h2>LAMMPS minimization parameters<a class="headerlink" href="#lammps-minimization-parameters" title="Permalink to this headline">¶</a></h2>
<p>Specifies the run parameters associated with an energy/force
minimization in LAMMPS.</p>
<ul class="simple">
<li><p><strong>energytolerance</strong>: specifies the energy tolerance to use for the
minimization. This value is unitless and corresponds to the etol term
for the <a class="reference external" href="http://lammps.sandia.gov/doc/minimize.html">LAMMPS minimize
command.</a> Default
value is 0.</p></li>
<li><p><strong>forcetolerance</strong>: specifies the force tolerance to use for the
minimization. This value is in force units and corresponds to the
ftol term for the <a class="reference external" href="http://lammps.sandia.gov/doc/minimize.html">LAMMPS minimize
command.</a> Default
value is ‘1.0e-10 eV/angstrom’.</p></li>
<li><p><strong>maxiterations</strong>: specifies the maximum number of iterations to use
for the minimization. This value corresponds to the maxiter term for
the <a class="reference external" href="http://lammps.sandia.gov/doc/minimize.html">LAMMPS minimize
command.</a> Default
value is 1000.</p></li>
<li><p><strong>maxevaluations</strong>: specifies the maximum number of iterations to use
for the minimization. This value corresponds to the maxeval term for
the <a class="reference external" href="http://lammps.sandia.gov/doc/minimize.html">LAMMPS minimize
command.</a> Default
value is 10000.</p></li>
<li><p><strong>maxatommotion</strong>: specifies the maximum distance that any atom can
move during a minimization iteration. This value is in units length
and corresponds to the dmax term for the <a class="reference external" href="http://lammps.sandia.gov/doc/min_modify.html">LAMMPS min_modify
command.</a> Default
value is ‘0.01 angstrom’.</p></li>
</ul>
</div>
<div class="section" id="run-parameters">
<h2>Run Parameters<a class="headerlink" href="#run-parameters" title="Permalink to this headline">¶</a></h2>
<p>Provides parameters specific to the calculation at hand.</p>
<ul class="simple">
<li><p><strong>annealtemperature</strong>: specifies the temperature at which to anneal
the dislocation system.</p></li>
<li><p><strong>annealsteps</strong>: specifies how many MD steps to perform at the anneal
temperature before running the energy/force minimization. Default
value is 0 if annealtemperature=0, and 10,000 if annealtemperature &gt;
0.</p></li>
<li><p><strong>randomseed</strong>: provides a random number seed to generating the
initial atomic velocities. Default value gives a random number as the
seed.</p></li>
<li><p><strong>dislocation_boundaryshape</strong>: ‘box’ or ‘cylinder’ specifying the
resulting shape of the active region after defining the boundary
atoms. For ‘box’, the boundary width is constant at the two
non-periodic box edges. For ‘cylinder’, the active region is a
cylinder centered around the dislocation line. Default value is
‘cylinder’.</p></li>
<li><p><strong>dislocation_boundarywidth</strong>: floating point number specifying the
minimum thickness of the boundary region.</p></li>
<li><p><strong>dislocation_boundaryscale</strong>: boolean indicating if the boundary
width is taken as absolute (False) or should be scaled by the loaded
unit cell’s a lattice parameter.</p></li>
</ul>
</div>
</div>


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  <h3><a href="../../index.html">Table of Contents</a></h3>
  <ul>
<li><a class="reference internal" href="#">Input script parameters</a><ul>
<li><a class="reference internal" href="#global-metadata-parameters">Global metadata parameters</a></li>
<li><a class="reference internal" href="#command-lines-for-lammps-and-mpi">Command lines for LAMMPS and MPI</a></li>
<li><a class="reference internal" href="#potential-definition-and-directory-containing-associated-files">Potential definition and directory containing associated files</a></li>
<li><a class="reference internal" href="#initial-system-configuration-to-load">Initial system configuration to load</a></li>
<li><a class="reference internal" href="#elastic-constants-parameters">Elastic constants parameters</a></li>
<li><a class="reference internal" href="#dislocation-defect-parameters">Dislocation defect parameters</a></li>
<li><a class="reference internal" href="#units-for-input-output-values">Units for input/output values</a></li>
<li><a class="reference internal" href="#lammps-minimization-parameters">LAMMPS minimization parameters</a></li>
<li><a class="reference internal" href="#run-parameters">Run Parameters</a></li>
</ul>
</li>
</ul>

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